1J3R | pdb_00001j3r

Crystal structure of Thermococcus litoralis phosphogrucose isomerase complexed with gluconate-6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb1J3R/pdb

• Classification: ISOMERASE
• Organism(s): Thermococcus litoralis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-02-11 Released: 2004-02-24 
• Deposition Author(s): Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.263 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a novel cupin-type phosphoglucose isomerase

Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.11 kDa 
• Atom Count: 3,291 
• Modeled Residue Count: 372 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglucose Isomerase	A, B	190	Thermococcus litoralis	Mutation(s): 0  EC: 5.3.1.9
UniProt
Find proteins for P84140 (Thermococcus litoralis) Explore P84140  Go to UniProtKB:  P84140

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6PG	C [auth A], E [auth B]	6-PHOSPHOGLUCONIC ACID C6 H13 O10 P BIRSGZKFKXLSJQ-SQOUGZDYSA-N
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.263 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.67	α = 90
b = 80.23	β = 90
c = 130.04	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-24 
Deposition Author(s): Jeong, J.-J., Fushinobu, S., Ito, S., Hidaka, M., Shoun, H., Wakagi, T.

Revision History  

• Version 1.0: 2004-02-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description